Base Info

An object of class Seurat 52787 features across 316546 samples within 2 assays Active assay: SCT (25520 features, 3000 variable features) 1 other assay present: RNA 3 dimensional reductions calculated: pca, umap, tsne

The Seurat object was generated with Seurat 3.1.4.

Table of Data

Class Data

Tissue Data

Annotated Cell Types

Calculated Clusters

Interactive Plot

Downsampled to 5000 cells. Hover over point for details.

Environment

## R version 3.6.3 (2020-02-29)
## Platform: x86_64-apple-darwin18.7.0 (64-bit)
## Running under: macOS Mojave 10.14.6
## 
## Matrix products: default
## BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
## LAPACK: /usr/local/Cellar/openblas/0.3.9/lib/libopenblasp-r0.3.9.dylib
## 
## locale:
## [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] future_1.17.0     sctransform_0.2.1 gsubfn_0.7        proto_1.0.0       DropSeq.util_2.0  Matrix_1.2-18     data.table_1.12.8
##  [8] R.matlab_3.6.2    Seurat_3.1.5      plotly_4.9.2.1    knitr_1.28        dplyr_0.8.5       ggplot2_3.3.0     rmarkdown_2.1    
## 
## loaded via a namespace (and not attached):
##  [1] nlme_3.1-147        tsne_0.1-3          bitops_1.0-6        RcppAnnoy_0.0.16    RColorBrewer_1.1-2  httr_1.4.1         
##  [7] tools_3.6.3         R6_2.4.1            irlba_2.3.3         KernSmooth_2.23-16  uwot_0.1.8          lazyeval_0.2.2     
## [13] colorspace_1.4-1    npsurv_0.4-0        withr_2.2.0         tidyselect_1.0.0    gridExtra_2.3       compiler_3.6.3     
## [19] labeling_0.3        caTools_1.18.0      scales_1.1.0        lmtest_0.9-37       ggridges_0.5.2      pbapply_1.4-2      
## [25] stringr_1.4.0       digest_0.6.25       R.utils_2.9.2       pkgconfig_2.0.3     htmltools_0.4.0     htmlwidgets_1.5.1  
## [31] rlang_0.4.5         farver_2.0.3        zoo_1.8-7           jsonlite_1.6.1      crosstalk_1.1.0.1   ica_1.0-2          
## [37] gtools_3.8.2        R.oo_1.23.0         magrittr_1.5        patchwork_1.0.0     Rcpp_1.0.4.6        munsell_0.5.0      
## [43] ape_5.3             reticulate_1.15     R.methodsS3_1.8.0   lifecycle_0.2.0     stringi_1.4.6       yaml_2.2.1         
## [49] MASS_7.3-51.5       gplots_3.0.3        Rtsne_0.15          plyr_1.8.6          grid_3.6.3          parallel_3.6.3     
## [55] gdata_2.18.0        listenv_0.8.0       ggrepel_0.8.2       crayon_1.3.4        lattice_0.20-41     cowplot_1.0.0      
## [61] splines_3.6.3       pillar_1.4.3        igraph_1.2.5        future.apply_1.5.0  reshape2_1.4.4      codetools_0.2-16   
## [67] leiden_0.3.3        glue_1.4.0          evaluate_0.14       lsei_1.2-0          vctrs_0.2.4         png_0.1-7          
## [73] gtable_0.3.0        RANN_2.6.1          purrr_0.3.4         tidyr_1.0.2         assertthat_0.2.1    xfun_0.13          
## [79] rsvd_1.0.3          survival_3.1-12     viridisLite_0.3.0   tibble_3.0.1        cluster_2.1.0       globals_0.12.5     
## [85] fitdistrplus_1.0-14 ellipsis_0.3.0      ROCR_1.0-7